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annotate Framework/Toolbox/Slice.cpp @ 120:063f7f3d9f14 wasm

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fix 3d locations of the doses
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 04 Oct 2017 15:51:34 +0200
parents ba83e38cf3ff
children e66b2c757790
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017 Osimis, Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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21
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22 #include "Slice.h"
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23
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24 #include "../Enumerations.h"
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25
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26 #include <Core/Logging.h>
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27 #include <Core/OrthancException.h>
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28 #include <Core/Toolbox.h>
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29
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30 #include <boost/lexical_cast.hpp>
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31
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32 namespace OrthancStone
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33 {
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34 static bool ParseDouble(double& target,
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35 const std::string& source)
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36 {
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37 try
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38 {
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39 target = boost::lexical_cast<double>(source);
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40 return true;
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41 }
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42 catch (boost::bad_lexical_cast&)
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43 {
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44 return false;
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45 }
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46 }
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47
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48 bool Slice::ComputeRTDoseGeometry(const Orthanc::DicomMap& dataset,
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49 unsigned int frame)
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50 {
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51 // http://dicom.nema.org/medical/Dicom/2016a/output/chtml/part03/sect_C.8.8.3.2.html
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52
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53 std::string increment, offsetTag;
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54
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55 if (!dataset.CopyToString(increment, Orthanc::DICOM_TAG_FRAME_INCREMENT_POINTER, false) ||
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56 !dataset.CopyToString(offsetTag, Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, false))
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57 {
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58 LOG(ERROR) << "Cannot read the \"GridFrameOffsetVector\" tag, check you are using Orthanc >= 1.3.1";
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59 return false;
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60 }
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61
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62 Orthanc::Toolbox::ToUpperCase(increment);
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63 if (increment != "3004,000C" ||
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64 offsetTag.empty())
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65 {
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66 return false;
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67 }
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69 std::vector<std::string> offsets;
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70 Orthanc::Toolbox::TokenizeString(offsets, offsetTag, '\\');
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71
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72 if (frameCount_ <= 1 ||
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73 offsets.size() != frameCount_ ||
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74 frame >= frameCount_)
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75 {
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76 LOG(ERROR) << "No information about the 3D location of some slice(s) in a RT DOSE";
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77 return false;
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78 }
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79
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80 double offset0, offset1, z;
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81
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82 if (!ParseDouble(offset0, offsets[0]) ||
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83 !ParseDouble(offset1, offsets[1]) ||
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84 !ParseDouble(z, offsets[frame]))
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85 {
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86 LOG(ERROR) << "Invalid syntax";
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87 return false;
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88 }
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89
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90 if (!GeometryToolbox::IsCloseToZero(offset0))
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91 {
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92 LOG(ERROR) << "Invalid syntax";
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93 return false;
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94 }
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95
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96 geometry_ = CoordinateSystem3D(geometry_.GetOrigin() + z * geometry_.GetNormal(),
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97 //+ 650 * geometry_.GetAxisX(),
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98 geometry_.GetAxisX(),
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99 geometry_.GetAxisY());
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100
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101 thickness_ = offset1 - offset0;
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102 if (thickness_ < 0)
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103 {
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104 thickness_ = -thickness_;
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105 }
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106
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107 printf("%d: %f %f %f\n", frame_, geometry_.GetOrigin()[0], geometry_.GetOrigin()[1], geometry_.GetOrigin()[2]);
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108 //printf("%f %f %f\n", pixelSpacingX_, pixelSpacingY_, thickness_);
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109
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110 return true;
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111 }
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114 bool Slice::ParseOrthancFrame(const Orthanc::DicomMap& dataset,
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115 const std::string& instanceId,
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116 unsigned int frame)
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117 {
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118 orthancInstanceId_ = instanceId;
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119 frame_ = frame;
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120 type_ = Type_OrthancDecodableFrame;
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121 imageInformation_.reset(new Orthanc::DicomImageInformation(dataset));
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122
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123 if (!dataset.CopyToString(sopClassUid_, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) ||
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124 sopClassUid_.empty())
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125 {
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126 LOG(ERROR) << "Instance without a SOP class UID";
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127 return false;
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128 }
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130 if (!dataset.ParseUnsignedInteger32(frameCount_, Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))
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131 {
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132 frameCount_ = 1; // Assume instance with one frame
73
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133 }
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134
117
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diff changeset
135 if (frame >= frameCount_)
73
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136 {
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137 return false;
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138 }
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139
118
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diff changeset
140 if (!dataset.ParseUnsignedInteger32(width_, Orthanc::DICOM_TAG_COLUMNS) ||
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diff changeset
141 !dataset.ParseUnsignedInteger32(height_, Orthanc::DICOM_TAG_ROWS))
73
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142 {
117
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diff changeset
143 return false;
73
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144 }
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145
117
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diff changeset
146 thickness_ = 100.0 * std::numeric_limits<double>::epsilon();
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diff changeset
147
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diff changeset
148 std::string tmp;
118
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diff changeset
149 if (dataset.CopyToString(tmp, Orthanc::DICOM_TAG_SLICE_THICKNESS, false))
117
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150 {
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151 if (!tmp.empty() &&
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152 !ParseDouble(thickness_, tmp))
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153 {
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154 return false; // Syntax error
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155 }
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156 }
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157
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158 converter_.ReadParameters(dataset);
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159
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160 GeometryToolbox::GetPixelSpacing(pixelSpacingX_, pixelSpacingY_, dataset);
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161
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162 std::string position, orientation;
118
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diff changeset
163 if (dataset.CopyToString(position, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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diff changeset
164 dataset.CopyToString(orientation, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
73
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165 {
110
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166 geometry_ = CoordinateSystem3D(position, orientation);
117
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167
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168 bool ok = true;
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169 SopClassUid tmp;
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170
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171 if (StringToSopClassUid(tmp, sopClassUid_))
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172 {
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173 switch (tmp)
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174 {
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175 case SopClassUid_RTDose:
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176 type_ = Type_OrthancRawFrame;
118
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177 ok = ComputeRTDoseGeometry(dataset, frame);
117
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178 break;
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179
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180 default:
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181 break;
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182 }
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183 }
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184
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185 if (!ok)
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186 {
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187 LOG(ERROR) << "Cannot deduce the 3D location of frame " << frame
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188 << " in instance " << instanceId << ", whose SOP class UID is: " << sopClassUid_;
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189 return false;
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190 }
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191 }
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192
117
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193 return true;
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194 }
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195
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196
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197 const std::string Slice::GetOrthancInstanceId() const
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198 {
117
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199 if (type_ == Type_OrthancDecodableFrame ||
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diff changeset
200 type_ == Type_OrthancRawFrame)
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201 {
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202 return orthancInstanceId_;
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203 }
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204 else
73
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205 {
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206 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
117
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diff changeset
207 }
73
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208 }
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parents:
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209
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210
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211 unsigned int Slice::GetFrame() const
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212 {
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213 if (type_ == Type_Invalid)
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214 {
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215 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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216 }
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parents:
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217
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218 return frame_;
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219 }
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diff changeset
220
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221
110
53025eecbc95 renamed SliceGeometry as CoordinateSystem3D
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parents: 102
diff changeset
222 const CoordinateSystem3D& Slice::GetGeometry() const
73
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223 {
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224 if (type_ == Type_Invalid)
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225 {
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diff changeset
226 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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227 }
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parents:
diff changeset
228
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diff changeset
229 return geometry_;
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parents:
diff changeset
230 }
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231
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parents:
diff changeset
232
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diff changeset
233 double Slice::GetThickness() const
ffa6dded91bd reorganization
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234 {
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parents:
diff changeset
235 if (type_ == Type_Invalid)
ffa6dded91bd reorganization
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parents:
diff changeset
236 {
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diff changeset
237 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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238 }
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parents:
diff changeset
239
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diff changeset
240 return thickness_;
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parents:
diff changeset
241 }
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parents:
diff changeset
242
ffa6dded91bd reorganization
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parents:
diff changeset
243
ffa6dded91bd reorganization
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parents:
diff changeset
244 double Slice::GetPixelSpacingX() const
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parents:
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245 {
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parents:
diff changeset
246 if (type_ == Type_Invalid)
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parents:
diff changeset
247 {
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diff changeset
248 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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249 }
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parents:
diff changeset
250
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diff changeset
251 return pixelSpacingX_;
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parents:
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252 }
ffa6dded91bd reorganization
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parents:
diff changeset
253
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254
ffa6dded91bd reorganization
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parents:
diff changeset
255 double Slice::GetPixelSpacingY() const
ffa6dded91bd reorganization
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parents:
diff changeset
256 {
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parents:
diff changeset
257 if (type_ == Type_Invalid)
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parents:
diff changeset
258 {
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parents:
diff changeset
259 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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260 }
ffa6dded91bd reorganization
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parents:
diff changeset
261
ffa6dded91bd reorganization
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parents:
diff changeset
262 return pixelSpacingY_;
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parents:
diff changeset
263 }
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
265
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
266 unsigned int Slice::GetWidth() const
ffa6dded91bd reorganization
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parents:
diff changeset
267 {
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parents:
diff changeset
268 if (type_ == Type_Invalid)
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parents:
diff changeset
269 {
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diff changeset
270 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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271 }
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parents:
diff changeset
272
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273 return width_;
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parents:
diff changeset
274 }
ffa6dded91bd reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
275
ffa6dded91bd reorganization
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parents:
diff changeset
276
ffa6dded91bd reorganization
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parents:
diff changeset
277 unsigned int Slice::GetHeight() const
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parents:
diff changeset
278 {
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parents:
diff changeset
279 if (type_ == Type_Invalid)
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parents:
diff changeset
280 {
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diff changeset
281 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents:
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282 }
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parents:
diff changeset
283
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284 return height_;
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285 }
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286
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287
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288 const DicomFrameConverter& Slice::GetConverter() const
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289 {
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290 if (type_ == Type_Invalid)
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291 {
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292 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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293 }
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294
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295 return converter_;
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296 }
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297
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298
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299 bool Slice::ContainsPlane(const CoordinateSystem3D& plane) const
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300 {
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301 if (type_ == Type_Invalid)
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302 {
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303 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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304 }
101
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305
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306 bool opposite;
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307 return (GeometryToolbox::IsParallelOrOpposite(opposite,
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308 GetGeometry().GetNormal(),
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309 plane.GetNormal()) &&
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310 GeometryToolbox::IsNear(GetGeometry().ProjectAlongNormal(GetGeometry().GetOrigin()),
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311 GetGeometry().ProjectAlongNormal(plane.GetOrigin()),
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312 thickness_ / 2.0));
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313 }
102
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314
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315
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316 void Slice::GetExtent(std::vector<Vector>& points) const
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317 {
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318 double sx = GetPixelSpacingX();
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319 double sy = GetPixelSpacingY();
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320 double w = static_cast<double>(GetWidth());
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321 double h = static_cast<double>(GetHeight());
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322
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323 points.clear();
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324 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, -0.5 * sy));
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325 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, -0.5 * sy));
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326 points.push_back(GetGeometry().MapSliceToWorldCoordinates(-0.5 * sx, (h - 0.5) * sy));
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327 points.push_back(GetGeometry().MapSliceToWorldCoordinates((w - 0.5) * sx, (h - 0.5) * sy));
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328 }
119
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329
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330
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331 const Orthanc::DicomImageInformation& Slice::GetImageInformation() const
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332 {
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333 if (imageInformation_.get() == NULL)
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334 {
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335 // Only available if constructing the "Slice" object with a DICOM map
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336 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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337 }
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338 else
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339 {
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340 return *imageInformation_;
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341 }
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342 }
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343 }